Two. Hook the menu into a theme hook location
( You could replace the 2nd step with the template code which displays the menu however this is not best practice when modifying Genesis and reserved for parent theme development)

You can wrap each in an existing class or wrap the lot in an existing or new menu class.

Clearly, these are not the only methods you can use to add new menus in WordPress or Genesis however its a good option for child theme users where Genesis supports the use of custom functions rather then editing parent theme template files.

The Genesis framework in this question came after I posted my answer. Anyway, the statement about registering menus always in init and not in after_theme_setup is not true. You can see how wordpress core themes register menus in after_theme_setup as well in some oficial documentation pages like codex.wordpress.org/Plugin_API/Action_Reference/…. In fact, navigation menus are defined by Wordpress as a "theme feature", so after_theme_setup is very appropiate hook.
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cybmetaFeb 2 '14 at 18:01

Its not the hook the WordPress Codex uses in its working examples.
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Brad DaltonFeb 3 '14 at 8:39

Then, in the admin menu manager you can build the menu and assing it to the new menu location you have previously register. After that, you can render the menu where you want it to be displayed in your theme: